Cotranslational folding in ab initio protein structure prediction and applications in de novo design;

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PROTACs (proteolysis-targeting chimera) are heterobifunctional molecules. They function by binding to a protein of interest (POI) and an E3 ligase. Bringing the POI into close proximity with the E3 ligase leads to polyubiquitination, which marks the POI for degradation by the proteosome. This mechanism of action makes PROTAC molecules exciting candidates for therapies which require long-term downregulation of a specific protein [1] [2].Many PROTAC molecules are derived from small molecules with known protein binding properties. A frequent approach is to tether a known small molecule E3 ligase binder to a different small molecule that is known to bind the protein of interest via a linker region (usually polyethylene glycol, or PEG).This project will be concerned with a smaller class of molecules known as IMIDs (immunomodulatory imide drugs). Members of this drug class include thalidomide, lenalidomide, and pomalidomide. Although not structurally similar to the more traditional chimeric PROTAC molecules, it is now known that IMIDs exhibit their pharmaceutical effects via a PROTAC-like mechanism. The imide component of the molecule - acting as an analogue of the biomolecule uridine - binds to the E3 ligase protein cereblon in a triple tryptophan hydrophobic pocket. The phthalimide half of the molecule, protruding out from the cereblon E3 ligase protein, alters the surface topology of cereblonFigure 1 PROTACS mechanism of action: In the absence of the protac molecule, the target protein is not degraded; in the presence of the protac, the target protein is linked to an E3 ligase, which marks it for degradation via polyubiquitination [13]such that it will now bind with a variety of other proteins, which all become marked for degradation via the aforementioned route.Work by GSK has explored the conserved features found amongst these target proteins in nature. Although diverse in overall shape, these proteins all share a small motif which binds to the IMID/cereblon complex. This motif is not conserved in terms of primary sequence, but is structurally analogous in each case. There is also a conserved glycine residue, which accommodates binding of the phthalimde motif of the IMID. Any residue other than glycine in this position would be too sterically crowded.Tests carried out by GSK have shown that this shared motif, hereafter referred to as a degron, can be added to a protein and used as a tag for degradation in the presence of an IMID drug. This approach has been named IPID (IMID Proximity Induced Degradation). Assays involving recombinant GFP-degron hybrids with variable GlySer linker lengths demonstrate the proof of concept.A current research goal at GSK is to explore the possibility of including this switch in CAR-T cell therapy (chimeric antigen receptor T cell therapy), a form of immunotherapy where T cells are modified to recognise and destroy the patient's own cancer cells. The protein through which this is achieved comprises of the scFv region of a monoclonal antibody, fused to a transmembrane domain